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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 431 by mmeineke, Thu Mar 27 22:16:27 2003 UTC vs.
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 <  int i, j;
69 >  ExtendedSystem* the_extendedsystem;
70 >  int i, j, k, globalAtomIndex;
71  
72    // get the stamps and globals;
73    the_stamps = stamps;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
160 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 228 | Line 298 | void SimSetup::createSim( void ){
298    simnfo->n_torsions = tot_torsions;
299    simnfo->n_SRI = tot_SRI;
300    simnfo->n_mol = tot_nmol;
301 +  simnfo->molMembershipArray = new int[tot_atoms];
302  
232 –  
303   #ifdef IS_MPI
304  
305    // divide the molecules among processors here.
306    
307    mpiSim = new mpiSimulation( simnfo );
308    
239 –  
240 –
309    globalIndex = mpiSim->divideLabor();
310  
243 –
244 –
311    // set up the local variables
312    
313    int localMol, allMol;
# Line 256 | Line 322 | void SimSetup::createSim( void ){
322    local_bonds = 0;
323    local_bends = 0;
324    local_torsions = 0;
325 +  globalAtomIndex = 0;
326 +
327 +
328    for( i=0; i<n_components; i++ ){
329  
330      for( j=0; j<components_nmol[i]; j++ ){
331        
332 <      if( mol2proc[j] == worldRank ){
332 >      if( mol2proc[allMol] == worldRank ){
333          
334          local_atoms +=    comp_stamps[i]->getNAtoms();
335          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 337 | void SimSetup::createSim( void ){
337          local_torsions += comp_stamps[i]->getNTorsions();
338          localMol++;
339        }      
340 <      allMol++;
340 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
341 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
342 >        globalAtomIndex++;
343 >      }
344 >
345 >      allMol++;      
346      }
347    }
348    local_SRI = local_bonds + local_bends + local_torsions;
349    
350 +  if (worldRank != 0) {
351 +    for (i =0; i < tot_atoms; i++){
352 +      std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
353 +    }
354 +  }
355  
356    simnfo->n_atoms = mpiSim->getMyNlocal();  
357    
# Line 316 | Line 395 | void SimSetup::createSim( void ){
395      
396      if(mol2proc[i] == worldRank ){
397        the_molecules[molIndex].setStampID( molCompType[i] );
398 +      the_molecules[molIndex].setMyIndex( molIndex );
399 +      the_molecules[molIndex].setGlobalIndex( i );
400        molIndex++;
401      }
402    }
# Line 323 | Line 404 | void SimSetup::createSim( void ){
404   #else // is_mpi
405    
406    molIndex = 0;
407 +  globalAtomIndex = 0;
408    for(i=0; i<n_components; i++){
409      for(j=0; j<components_nmol[i]; j++ ){
410        the_molecules[molIndex].setStampID( i );
411 +      the_molecules[molIndex].setMyIndex( molIndex );
412 +      the_molecules[molIndex].setGlobalIndex( molIndex );
413 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
414 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
415 +        globalAtomIndex++;
416 +      }
417        molIndex++;
418      }
419    }
# Line 336 | Line 424 | void SimSetup::createSim( void ){
424  
425    if( simnfo->n_SRI ){
426      
339 –    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
340 –    
427      Exclude::createArray(simnfo->n_SRI);
428      the_excludes = new Exclude*[simnfo->n_SRI];
429      for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
430      simnfo->globalExcludes = new int;
431 <    simnfo->n_exclude = tot_SRI;
431 >    simnfo->n_exclude = simnfo->n_SRI;
432    }
433    else{
434      
# Line 462 | Line 548 | void SimSetup::createSim( void ){
548      }
549      simnfo->dielectric = the_globals->getDielectric();  
550    } else {
551 <    if (simnfo->n_dipoles) {
551 >    if (usesDipoles) {
552        
553        if( !the_globals->haveECR() ){
554          sprintf( painCave.errMsg,
555 <                 "SimSetup Warning: using default value of 1/2 the smallest"
555 >                 "SimSetup Warning: using default value of 1/2 the smallest "
556                   "box length for the electrostaticCutoffRadius.\n"
557                   "I hope you have a very fast processor!\n");
558          painCave.isFatal = 0;
# Line 482 | Line 568 | void SimSetup::createSim( void ){
568        
569        if( !the_globals->haveEST() ){
570          sprintf( painCave.errMsg,
571 <                 "SimSetup Warning: using default value of 5% of the"
571 >                 "SimSetup Warning: using default value of 5%% of the "
572                   "electrostaticCutoffRadius for the "
573                   "electrostaticSkinThickness\n"
574                   );
# Line 657 | Line 743 | void SimSetup::createSim( void ){
743  
744   //   new AllLong( simnfo );
745  
660 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
661 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
746  
747 <
747 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
748 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
749 >  }
750 >  else if( !strcmp( force_field, "LJ" ) ){
751 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
752 >  }
753 >  else {
754 >    std::cerr << "I'm a bug.\n";
755 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
756 >  }
757 > #ifdef IS_MPI
758 >  mpiSim->mpiRefresh();
759 > #endif
760  
761    // initialize the Fortran
762 <  
762 >
763 >
764    simnfo->refreshSim();
765    
766    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 782 | Line 879 | void SimSetup::makeMolecules( void ){
879        theBonds[j].a = currentBond->getA() + atomOffset;
880        theBonds[j].b = currentBond->getB() + atomOffset;
881  
882 <      exI = theBonds[i].a;
883 <      exJ = theBonds[i].b;
882 >      exI = theBonds[j].a;
883 >      exJ = theBonds[j].b;
884  
885        // exclude_I must always be the smaller of the pair
886        if( exI > exJ ){
# Line 799 | Line 896 | void SimSetup::makeMolecules( void ){
896        
897        the_excludes[j+excludeOffset]->setPair( exI, exJ );
898   #else  // isn't MPI
899 +
900        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
901   #endif  //is_mpi
902      }
# Line 836 | Line 934 | void SimSetup::makeMolecules( void ){
934                
935              default:
936                sprintf( painCave.errMsg,
937 <                       "SimSetup Error: ghostVectorSource was neiter a "
937 >                       "SimSetup Error: ghostVectorSource was neither a "
938                         "double nor an int.\n"
939                         "-->Bend[%d] in %s\n",
940                         j, comp_stamps[stampID]->getID() );
# Line 930 | Line 1028 | void SimSetup::makeMolecules( void ){
1028  
1029  
1030      the_molecules[i].initialize( info );
1031 +
1032 +
1033      atomOffset += info.nAtoms;
1034      delete[] theBonds;
1035      delete[] theBends;
1036      delete[] theTorsions;
1037    }
1038 +
1039 + #ifdef IS_MPI
1040 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1041 +  MPIcheckPoint();
1042 + #endif // is_mpi
1043  
1044    // clean up the forcefield
1045    the_ff->calcRcut();
1046    the_ff->cleanMe();
1047 +
1048   }
1049  
1050   void SimSetup::initFromBass( void ){

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